• heatmaply
  • " />
    suppressPackageStartupMessages({
        library("SummarizedExperiment")
        library("plotlyutils")
        library("heatmaply")
        library("limma")
    })
    • TCGA GBM data
    • Glycolysis gene signature “correlated with IDH1 mutation in GBM” taken from Chen et al. (2017)
    ## https://www.sciencedirect.com/science/article/pii/S1673852717301492
    df <- colData(GBMdata)[, "subtype_IDH.status", drop = FALSE]
    colnames(df) <- "IDH1 status"
    gene_signature <- c("ALDOB",
        "ENO1",
        "GALM",
        "GAPDH",
        "HK2",
        "HK3",
        "LDHA",
        "LDHB",
        "PKLR")
    raw_mat <- assay(GBMdata)
    raw_median_mat <- sweep(raw_mat, 1, rowMedians(raw_mat))
    heatmaply_cor(cor(raw_median_mat[gene_signature, ]),
        row_side_colors = df,
        plot_method = "plotly",
        showticklabels = c(FALSE, FALSE))
    voom_mat <- voomed_GBM$E
    voom_median_mat <- sweep(voom_mat, 1, rowMedians(voom_mat))
    max <- max(abs(voom_median_mat[gene_signature, ]))
    heatmaply(t(voom_median_mat[gene_signature, ]),
        row_side_colors = df,
        showticklabels = c(TRUE, FALSE),
        limits = c(-max, max),
        plot_method = "plotly",
        col = cool_warm)